Source code for pygfa.graph_element.parser.gap

import re

from pygfa.graph_element.parser import line, field_validator as fv

class Gap(line.Line):

    def __init__(self):
        super().__init__('G')

    REQUIRED_FIELDS = { \
    'gid' : fv.GFA2_OPTIONAL_ID, \
    'sid1' : fv.GFA2_REFERENCE, \
    'sid2' : fv.GFA2_REFERENCE, \
    'distance' : fv.GFA2_INT, \
    'variance' : fv.GFA2_OPTIONAL_INT \
    }

    @classmethod
    def from_string(cls, string):
        """Extract the Gap fields from the string.

        The string can contains the G character at the begin or can
        only contains the fields of the Gap directly.
        """
        if len(string.split()) == 0:
            raise line.InvalidLineError("Cannot parse the empty string.")
        fields = re.split('\t', string)
        gfields = []
        if fields[0] == 'G':
            fields = fields[1:]

        if len(fields) < len(cls.REQUIRED_FIELDS):
            raise line.InvalidLineError("The minimum number of field for "
                                        + "Gap line is not reached.")
        gap = Gap()

        gid_f = fv.validate(fields[0], cls.REQUIRED_FIELDS['gid'])
        gfields.append(line.Field('gid', gid_f))

        sid1_f = fv.validate(fields[1], cls.REQUIRED_FIELDS['sid1'])
        gfields.append(line.Field('sid1', sid1_f))

        sid2_f = fv.validate(fields[2], cls.REQUIRED_FIELDS['sid2'])
        gfields.append(line.Field('sid2', sid2_f))

        disp_f = fv.validate(fields[3], cls.REQUIRED_FIELDS['distance'])
        gfields.append(line.Field('distance', disp_f))

        variance_f = fv.validate(fields[4], cls.REQUIRED_FIELDS['variance'])
        gfields.append(line.Field('variance', variance_f))

        for field in fields[5:]:
            gfields.append(line.OptField.from_string(field))

        for field in gfields:
            gap.add_field(field)

        return gap

if __name__ == '__main__': # pragma: no cover
    pass